title: Cardiac Myoediting Mitigates Cardiomyopathy in Human and Mouse Models of Duchenne Muscular Dystrophy

city: Dallas

first: Miao

last: Cui

state: Texas

address: UT Southwestern Medical Center Department of Molecular Biology 6000 Harry Hines Blvd.

institute: UTSW

summary: Absence of the dystrophin gene in Duchenne muscular dystrophy (DMD) results in the degeneration of skeletal and cardiac muscles. Owing to advances in respiratory medicine, cardiomyopathy has become a significant aspect of the disease. While CRISPR/Cas9 genome editing technology holds great potential as a novel therapeutic avenue for DMD, little is known about the efficacy of correction of DMD using the CRISPR/Cas9 system in mitigating the cardiomyopathy phenotype in DMD. To define the effects of CRISPR/Cas9 genome editing on structural, functional and transcriptional dysregulation in DMD-associated cardiomyopathy. We generated induced pluripotent stem cells (iPSCs) from a patient with a deletion of exon 44 of the DMD gene (ΔEx44) and his healthy brother. Here, we targeted exon 45 of the DMD gene by CRISPR/Cas9 genome editing to generate corrected DMD (cDMD) iPSC lines, wherein the DMD open reading frame was restored via reframing (RF) or exon skipping (ES). While DMD cardiomyocytes (CMs) demonstrated morphologic, structural and functional deficits compared to control CMs, CMs from both cDMD lines were similar to control CMs. Bulk RNA-sequencing of DMD CMs showed transcriptional dysregulation consistent with dilated cardiomyopathy, which was mitigated in cDMD CMs. We then corrected DMD CMs by adenoviral delivery of Cas9/gRNA and showed that postnatal correction of DMD CMs reduces their arrhythmogenic potential. Single-nucleus RNA-sequencing of hearts showed reduced transcriptional dysregulation in CMs and fibroblasts in corrected mice compared with DMD mice, consistent with reduced histopathologic changes.We show that CRISPR/Cas9-mediated correction of DMD ΔEx44 mitigates structural, functional and transcriptional dysregulation consistent with dilated cardiomyopathy irrespective of how the protein reading frame is restored. We show that these effects extend to postnatal editing in iPSC-CMs and mice. These findings provide key insights into the utility of genome editing as a novel therapeutic for DMD-associated cardiomyopathy.

overall_design: Examination of transcriptome changes in cardiac cells from WT, DMD, and AAV-corrected DMD (cDMD) mouse hearts using snRNA-seq.

first: Ayhan

last: Atmanli

first: Rhonda

last: Bassel-Duby

first: Eric

last: Olson


title: The Rsm (Csr) post-transcriptional regulatory system directly controls CRISPR-Cas immunity

status: Public on Aug 02 2021

city: Dunedin

first: Peter

middle: Charles

last: Fineran

state: Otago

address: 720 Cumberland Street

department: Department of Microbiology and Immunology

country: New Zealand

institute: University of Otago

type: Expression profiling by high throughput sequencing

summary: RIP-seq analysis to identify RsmA bound RNAs using co-immunoprecipitation and sequencing in Serratia sp. ATCC 39006. We report the binding sites of RsmA (CsrA homologue) in Serratia sp. ATCC39006

overall_design:
RsmA was chromosomally tagged using 3xFLAG epitope at the C-terminus in Serratia sp. ATCC39006 wild-type cells and immunoprecipitated using anti-FLAG antibody,  untagged version of the wild-type Serratia sp. ATCC39006 strain was used as a control.  Lysates for immunoprecipitation for both untagged and RsmA-3xFLAG samples were prepared from  60 O.D. of bacteria grown to mid-log phase ( OD600 ≈ 0.6) . RNA was eluted from both untagged and RsmA-3xFLAG  samples to use for cDNA library preparation and sequencing.
RNA sequencing of RsmA (NMW7) and LacA strains of stationary phase (12h) cultures for identification of transcriptional changes due to RsmA mutation.

first: Aroa

middle: R

last: Campa

first: Leah

middle: M

last: Smith

first: Hannah

middle: G

last: Hampton

first: Sahil

last: Sharma

first: Simon

middle: A

last: Jackson

first: Thorsten

last: Bischler

first: Cynthia

middle: C


title: SMAD4 represses FOSL1 expression and pancreatic cancer metastatic colonization

city: BOSTON

first: William

last: Hahn

state: Massachusetts

address: 450 Brookline Avenue, Dana 1538

country: USA

institute: DANA-FARBER CANCER INSTITUTE

summary: Less than 8% of patients diagnosed with pancreatic ductal adenocarcinomas (PDAC) survive more than five years in part due to late stage diagnosis. Approximately half of PDAC patients exhibit loss of SMAD4, which correlates with increased metastatic disease. Here we demonstrate that SMAD4 is a suppressor of metastatic colonization. Using isogenic human PDAC cell lines expressing or lacking SMAD4, both in vitro and in vivo, we define SMAD4-dependent gene expression changes in metastatic lesions. We performed a pooled in vivo open reading frame (ORF) screen of SMAD4 transcriptional targets and identified genes that, induce tumor seeding and growth at secondary sites. We found that expression of the transcription factor FOSL1 was sufficient to drive metastatic colonization. SMAD4 directly binds and represses the activity of the FOSL1 enhancer. These studies demonstrate a direct role for SMAD4 in regulating metastatic colonization and identify FOSL1 as a SMAD4-regulated gene involved in PDAC progression.

overall_design: In vitro and in vivo manipulation of SMAD4 with and without TGFB

first: Chao

last: Dai

first: Jonathan

last: Rennhack


title: CRISPR-mediated activation of endogenous gene expression in the postnatal heart [ChIP-seq]

city: Goettingen

first: Laura

last: Zelarayan

state: Lower Saxony

address: Robert-Koch Strasse 40

department: Institute of Pharmacology and Toxicology

country: Germany

institute: University Medical Center, Goettingen

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Endogenous activation of Myocyte enhancer factor 2 D (Mef2d) and Krüppel-like factor 15 (Klf15) in the postnatal mouse heart by cardiomyocyte-specific CRISPRactivation (Myh6-dCas9VPR)
The aim of this experiment was to identify dCas9VPR on- and off-target chromatin association after gRNA delivery targeted to Myocyte enhancer factor 2 D (Mef2d) and Krüppel-like factor 15 (Klf15) in the postnatal mammalian heart. Saline injected Myh6-dCas9VPR transgenic mice were used to identify gRNA dependent and gRNA independent off-target sites.
Mice were injected with saline/AAV9 TRISPR Mef2d/AAV9 TRISPR Klf15 at P4 and sacrificed at P14. Hearts were minced and nuclei were isolated, sonicated and dCas9VPR bound regions were immunoprecipitated. dCas9VPR occupancy profiles were obtained using deep sequencing, in triplicates, using Illumina HiSeq4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by DESeq2. qPCR validation was performed using SYBR Green assays.
We present in this study a mouse model for cardiomyocyte-specific endogenous gene activation in the postnatal mammalian heart by CRISPR/dCas9VPR. As a proof of concept, we activated the pro-hypertrophic factor Myocyte enhancer factor 2 D (Mef2d) leading to functional decline, increased marker expression of heart failure as well as cardiomyocyte hypertrophy over a time course of 8 weeks. We furthermore observed no phenotypic consequence of constitutive dCas9VPR transgene expression in the postnatal heart. We therefore conclude, that the Myh6-dCas9VPR mouse model is a suitable tool for endogenous gene activation studies in the postnatal heart. We additionally activated Krüppel-like factor 15 (Klf15) in neonatal heart and confirmed increased Klf15 transcript levels. dCas9VPR-On-target association was confirmed by ChIP qPCRs and sequencing for both targets.

overall_design: dCas9 genomic occupancy profiling from Mef2d and Klf15 endogenous gene activation in the postnatal hearts versus controls.

first: Lavanya

last: Iyer

last: Schoger


title: CRISPR-mediated activation of endogenous gene expression in the postnatal heart

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: CRISPR-mediated activation of endogenous gene expression in the postnatal heart [RNA-seq]

summary:
Endogenous activation of Myocyte enhancer factor 2 D (Mef2d) in the postnatal mouse heart by cardiomyocyte-specific CRISPRactivation (Myh6-dCas9VPR)
The aim of this study was to compare endogenous gene activation of the pro-hypertrophic factor Myocyte enhancer factor 2 D (Mef2d) in the postnatal mammalian heart and experimental control groups including wild-type litter mates injected with saline, wild-type litter mates injected with AAV9 TRISPR Mef2d and transgenic litter mates injected with saline.
Mice were injected with saline/AAV9 TRISPR Mef2d at P4 and sacrificed 8 weeks later. RNA was isolated by TRIzol/Chloroform and isopropanol precipitation. Ventricular tissue mRNA profiles were obtained using deep sequencing, in triplicates, using Illumina HiSeq4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by DESeq2. qPCR validation was performed using SYBR Green assays.
We present in this study a mouse model for cardiomyocyte-specific endogenous gene activation in the postnatal mammalian heart by CRISPR/dCas9VPR. As a proof of concept, we activated the pro-hypertrophic factor Myocyte enhancer factor 2 D (Mef2d) leading to functional decline, increased marker expression of heart failure as well as cardiomyocyte hypertrophy over a time course of 8 weeks. We furthermore observed no phenotypic consequence of constitutive dCas9VPR transgene expression in the postnatal heart. We therefore conclude, that the Myh6-dCas9VPR mouse model is a suitable tool for endogenous gene activation studies in the postnatal heart.

overall_design: Transcriptome profiling from Mef2d endogenous gene activation in the postnatal hearts versus controls.


title: Distinct TCF7L2 genomic occupancies discern chromatin states in the neonatal and diseased mammalian myocardium


title: KRAS inhibitor-resistance in MET-amplified KRASG12C 1 non-small cell lung cancer induced by RAS- and non-RAS-mediated cell signaling mechanism

status: Public on Aug 01 2021

city: Osaka-Sayama

first: Toshiyuki

last: Takehara

state: Osaka

address: 377-2, Ohno-Higashi

department: Faculty of Medicine

country: Japan

institute: Kindai Universty Hospital

summary: Treatment with KRASG12C inhibitors such as sotorasib can produce substantial regression of tumors in some patients with non-small cell lung cancer (NSCLC). These patients require alternative treatment after acquiring resistance to the inhibitor. The mechanisms underlying this acquired resistance are unclear. The purpose of this study was to identify the mechanisms underlying acquired sotorasib resistance, and to explore potential treatments for rescuing patients with sotorasib-resistant KRASG12C NSCLC cells.

overall_design: H23ARC11 cell lines as resistant clones of sotorasib-sensitive KRAS G12C NSCLC H23 cells were obtained by exposing to increasing concentrations of sotorasib for nine months. Gene expression analysis was performed on ClariomS Human (Affymetrix) Chips.

first: Shinichiro

last: Suzuki

first: Kimio

last: Yonesaka

first: Takeshi

last: Teramura

first: Kazuhiko

last: Nakagawa


title: The immune heterogeneity between pulmonary adenocarcinoma and squamous cell carcinoma: a comprehensive analysis based on lncRNA model

city: Jinan

first: Jiajun

last: Du

address: 324 Jingwu Road

country: China

institute: Provincial Hospital Affiliated to Shandong University

summary: Adenocarcinoma (AD) and squamous carcinoma (SCC) are major types of lung cancer. Although they both belong to non-small cell lung cancer (NSCLC), the differences in clinical prognosis and molecular mechanism between them are remarkable. Recently, numerous studies proved that immune status of carcinoma patients influence deeply the clinical outcome. Based on the theory of “Immune edit”, many immunotherapies come out and tremendously extended the life of the patients. Thus, research on immune status is significant and essential. Our study aims to select specific lncRNAs which control the key immune-related genes to construct the risk model for AD and SCC respectively and the patients were divided into high- and low-risk groups based on risk score. The prognostic significance of risk score was validated by our own cohorts. Besides, The GSEA analysis suggested that immune response or process of AD patients in high-risk group was weaken while the situation is opposite for SCC cohort. The evaluation of immune infiltration reveled that the infiltrating degree of dendritic cell (DC cell) might be the important change for AD patients. In addition, the prediction of response to immune checkpoint inhibitors (ICIs) treatment, based on T cell immune dysfunction and exclusion (TIDE) and immunophenoscore (IPS), indicated that the reasons for the deterioration of the immune microenvironment were T cell exclusion in AD patients and T cell dysfunction in SCC patients and the high-risk patients with SCC might benefit from ICIs treatment. Furthermore, the prediction of downstream targets via The Cancer Proteome Atlas (TCPA) database and RNA-seq analysis based on transferred lung cancer cell line indicated that lINC00996 was potential to become the therapeutic target for AD patients.

overall_design: Construction of risk-socre models for AD and SCC patietns and exploraton the differences beween them.

first: Tao

last: Yan


title: Transcriptional analysis of beta-catenin overexpressing T cells

city: Syracuse

first: Mobin

last: Karimi

state: NY

address: 766 Irving Ave Suite 2281

department: Microbiology/Immunology

institute: Suny Upstate Medical University

summary: Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is one of the most widely applied forms of adaptive immunotherapy. Both the detrimental graft-versus-host disease (GVHD) and the beneficial graft-versus-leukemia (GVL) effects occurring after allo-HSCT are largely mediated by alloantigen-reactive donor T cells in the graft. Separating GVHD from GVL effects is a formidable challenge, and a greater understanding of donor T cell biology is required to accomplish the uncoupling of GVHD from GVL. Here, we tested a novel mouse model of transgenic over-expression of human β-catenin (Cat-Tg) in an allo-HSCT model. Our data show that T cells from Cat-Tg mice did not cause GVHD. Surprisingly, Cat-Tg T cells maintained the GVL effect. Donor T cells from Cat-Tg mice exhibited significantly lower inflammatory cytokine production and reduced donor T cell proliferation, while upregulating cytotoxic mediators that resulted in enhanced cytotoxicity. RNA sequencing data revealed changes in the expression of 1169 genes for CD4, and 1006 genes for CD8+T cells involved in essential aspects of immune response and GVHD pathophysiology. Transgenic over-expression of human β-catenin primarily affects CD8+ T cell phenotype. Altogether, our data suggest that β-catenin is a druggable target for developing therapeutic strategies to reduce GVHD while preserving the beneficial GVL effects following allo-HSCT treatment

overall_design: We analyzed FACS purified CD4 and CD8 T cells of 3 different human beta catenin overexpressing(Cat-Tg) and WT mouse, along with CD4 and CD8 T Cells of Cat-Tg and WT mouse that were initially transplanted into lethally irradiated recipent Balb/c mouse and were FACS purified after day 7 post transplant from the spleen of recipients.

first: Mahinbanu

last: Mammadli

first: Adam

last: Waickman


title: Distinct TCF7L2 genomic occupancies discern chromatin states in the neonatal and diseased mammalian myocardium [ChIP-Seq]

summary: In mammals, Wnt pathway is activated during both heart regeneration post-injury and disease. Our previous work described the role of nuclear Wnt effectors B-catenin and Transcription factor 7-like 2 (TCF7L2) in heart disease progression; revealing GATA4 as a Wnt-repressor in the healthy adult heart. However, there is an urgent need to dissect molecular players distinguishing regenerative vs. disease-specific responses. In this study, we report a GATA4-B-catenin interaction in the regenerative neonatal myocardium, despite high TCF7L2 expression. TCF7L2 displayed strikingly unique genomic occupancies: proximal in neonatal and distal in diseased hearts. Integrative genomic and transcriptomic analyses showed that TCF7L2 differentially occupied and regulated fatty acid metabolic genes in the neonatal; and cardiac developmental and vasculogenesis genes in the diseased hearts, clearly discerning these two cardiac states. De-novo motif search identified TEAD as a commonly enriched motif in both TCF7L2 and GATA4-bound regions in the neonatal hearts, suggesting its potential role in providing a regenerative context to this GATA4-B-catenin interaction. Altogether, our study mapped for the first time, novel genome-wide TCF7L2 and GATA4 targets in the neonatal hearts and identified stage-specific roles for the cardiac Wnt-GATA4 complex. These findings demonstrate strong context-specificity of the cardiac Wnt-nuclear complex, which can be further exploited for therapeutic avenues.

overall_design: Genome-wide TCF7L2, GATA4 and H3K27ac binding profiles in postnatal day 6 (P6) murine cardiac ventricles


title: Array-based genome-wide transcriptome analysis of the left atrial appendage for the difference between SR maintenance group and AF recurrence group

city: Sakai

first: OSAMU

last: ISHIBASHI

address: 1-1 Gakuen-cho, Naka-ku

department: Grad Sch Life & Environmental Sciences

institute: Osaka Prefecture University

summary: Atrial fibrillation (AF), which causes cardiogenic cerebral infarction, is the most common type of persistent arrhythmia, and its incidence increases with age. We performed a radial procedure using an RF ablation device to restore sinus rhythm (SR).

overall_design: Microarray analysis of the difference between the SR maintenance group (n=4) and the AF recurrence group (n=3) after Maze surgery was performed using FFPE samples of left atrial appendage.

first: Masahiro

last: Fujii

first: Tomoo

last: Jikuzono

first: Osamu

last: Ishibashi


title: Graft junction transcriptome between tomato and pepper over time

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary:
We report transcripts from tomato:tomato and pepper:pepper self-grafts, and tomato:pepper and pepper:tomato hetergrafts over 4 time points: 24 hours after grafting, 3 days after grafting,  5 day after grafting, and 2 weeks after grafting
Examination of 4 graft combinations over 4 time points

sample_organism:
Capsicum annuum
Solanum lycopersicum

platform_organism:
Capsicum annuum
Solanum lycopersicum

overall_design: Margaret, H, Frank

first: Hannah

last: Thomas


title: Multiple physiological roles of both specific and non-specific DNA binding modes of HU protein in Escherichia coli

city: Bethesda

first: Subhash

middle: (Optional)

last: Verma

state: MD

address: 37 Convent Drive, BLDG 37 Room 5138

institute: National Institutes of Health

summary: The histone-like protein HU is crucial for genome organization and the expression of many genes in Escherichia coli. HU binds DNA independent of any specific nucleotide sequence but exhibits two binding affinities; low-affinity to any B-DNA (non-specific) and high affinity to DNA with distortions like kinks and cruciforms (structure-specific). We validated and defined the three conserved lysine residues, K3, K18, and K83, in HU as critical amino acid residues for the non-specific binding and the conserved P63 together with the lysine residues critical for the structure-specific binding both in vitro and in vivo. By determining the effects of disrupting the two DNA binding modes on various HU-dependent physiological processes, we demonstrate that the DNA structure-specific binding regulates expression of many genes including those involved in DNA metabolic processes that control chromosome maintenance and partition. On the other hand, HU associates with the chromosome at numerous sites primarily through the lysines-mediated non-specific binding and control chromosome dynamics and structural maintenance. Thus, we demonstrate that two different DNA binding mode of HU plays separate roles: (i) The high-affinity DNA structure-specific binding regulates many distinct DNA metabolic processes, primarily through transcription regulation. (ii) Its low-affinity, non-specific binding directly helps general organization of the genome.

overall_design: Three biological replicates were analyzed for each strain

first: Sankar

last: Adhya


title: Endothelial Mekk3 alters fates of embryonic arterial endothelial cells

city: San Francisco

first: Qin

last: Zhu

state: CA

address: 600 Minnesota Street

institute: UCSF

summary: To examine how endothelial Mekk3 affects the cell and molecular transitions between endothelial (E), hemogenic endothelial (HE), and intra-aortic hematopoietic clusters (IAHC) cells, we profiled ~6,700 cells from wildtype embryos and ~3,200 cells from endothelial Mekk3 deleted embryos by single-cell RNA sequencing (scRNA-Seq). The cells were sorted from the caudal arteries (dorsal aorta, umbilical, vitelline arteries) of embryonic day (E) 9.5 mouse embryos. We identified a developmental alteration in endothelial to hematopoietic transition (EHT) and production of HE and IAHC in endothelial Mekk3 deleted embryos.

overall_design: Single cell RNA-Seq profiles of cells involved in endothelial to hematopoietic transition (EHT) from wildtype and endothelial Mekk3 deleted mouse embryos at embryonic day 9.5.

first: Mark

last: Kahn

first: Nancy

last: Speck

first: Kai

last: Tan


title: Distinct TCF7L2 genomic occupancies discern chromatin states in the neonatal and diseased mammalian myocardium [RNA-Seq]

first: Laura

last: Zelarayan

summary:
In mammals, Wnt pathway is activated during both heart regeneration post-injury and disease. Our previous work described the role of nuclear Wnt effectors B-catenin and Transcription factor 7-like 2 (TCF7L2) in heart disease progression; revealing GATA4 as a Wnt-repressor in the healthy adult heart. However, there is an urgent need to dissect molecular players distinguishing regenerative vs. disease-specific responses. In this study, we report a GATA4-B-catenin interaction in the regenerative neonatal myocardium, despite high TCF7L2 expression. TCF7L2 displayed strikingly unique genomic occupancies: proximal in neonatal and distal in diseased hearts. Integrative genomic and transcriptomic analyses showed that TCF7L2 differentially occupied and regulated fatty acid metabolic genes in the neonatal; and cardiac developmental and vasculogenesis genes in the diseased hearts, clearly discerning these two cardiac states. De-novo motif search identified TEAD as a commonly enriched motif in both TCF7L2 and GATA4-bound regions in the neonatal hearts, suggesting its potential role in providing a regenerative context to this GATA4-B-catenin interaction. Altogether, our study mapped for the first time, novel genome-wide TCF7L2 and GATA4 targets in the neonatal hearts and identified stage-specific roles for the cardiac Wnt-GATA4 complex. These findings demonstrate strong context-specificity of the cardiac Wnt-nuclear complex, which can be further exploited for therapeutic avenues.
Purpose: The aim of this study was to investigate the transcriptome profiles (RNA-seq) of WT postnatal day 6 murine cardiac ventricles; and compare them to our previously published (GSE97762) adult and diseased myocardium transcriptomes.
Methods: P6 cardiac ventricular tissue mRNA profiles were obtained using deep sequencing, in triplicates, using Illumina HiSeq4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by DESeq2. qPCR validation was performed using TaqMan and SYBR Green assays
Conclusions: Our study identified distinct transcriptomic signatures of P6 murine cardiac ventricles, in comparison to healthy or diseased adult heart. Particularly, despite high Wnt signaling activities and cardiomyocytes cell cycling in both P6 and diseased hearts, P6 hearts are regenerative in nature, while the diseased hearts are not.

overall_design: Gene expression profiling from murine P6 cardiac ventricles.

first: Lavanya

last: Iyer


title: RGC-32 acts as a hub to regulate the transcriptomic changes associated with astrocyte development and reactive astrocytosis

city: Baltimore

first: Horea

last: Rus

address: 655 W Baltimore St

department: Department of Neurology

institute: University of Maryland, School of Medicine

summary: Response Gene to Complement 32 (RGC-32) is an important mediator of the TGF-β signaling pathway, and an increasing amount of evidence implicates this protein in regulating astrocyte biology. We showed recently that spinal cord astrocytes in mice lacking RGC-32 display an immature phenotype reminiscent of progenitors and radial glia, with an overall elongated morphology, increased proliferative capacity, and increased expression of progenitor markers when compared to their wild-type (WT) counterparts that make them incapable of undergoing reactive changes during the acute phase of experimental autoimmune encephalomyelitis (EAE). Here, in order to decipher the molecular networks underlying RGC-32’s ability to regulate astrocytic maturation and reactivity, we performed next-generation sequencing of RNA from WT and RGC-32 knockout (KO) astrocytes, either unstimulated or stimulated with the pleiotropic cytokine TGF-β. Pathway enrichment analysis showed that RGC-32 is critical for the TGF-β-induced up-regulation of transcripts encoding proteins involved in brain development and tissue remodeling, such as axonal guidance molecules, transcription factors, extracellular matrix (ECM)-related proteins, and proteoglycans. Our next-generation sequencing of RNA analysis also demonstrated that a lack of RGC-32 results in a significant induction of WD repeat and FYVE domain-containing protein 1 (Wdfy1) and stanniocalcin-1 (Stc1). Immunohistochemical analysis of spinal cords isolated from normal adult mice and mice with EAE at the peak of disease showed that RGC-32 is necessary for the in vivo expression of ephrin receptor type A7 in reactive astrocytes, and that the lack of RGC-32 results in a higher number of homeodomain-only protein homeobox (HOPX)+ and CD133+ radial glia cells. Collectively, these findings suggest that RGC-32 plays a major role in modulating the transcriptomic changes in astrocytes that ultimately lead to molecular programs involved in astrocytic differentiation and reactive changes during neuroinflammation.

overall_design: Primary brain astrocyte mRNA profiles of 1-day old wild type and RGC-32 knock-out mice

first: Alexandru

last: Tatomir

first: Austin

last: Beltrand

first: Vinh

last: Nguyen

first: Jean-Paul

last: Courneya

first: Dallas

last: Boodhoo

first: Cornelia

last: Cudrici

first: Dafin

middle: F

last: Muresanu

first: Violeta

first: Tudor

last: Badea


title: Small RNA sequencing of cell RNA and extracellular vesicle (EV) RNA from MDA-MB-231-derived isogenic cells

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: To identify the cell miRNAs and EV miRNAs that are differentially expressed or secreted by the MDA-MB-231 metastatic breast cancer cells with genetic modifications, we profiled the small RNAs (between 17 and 52 nt) in cells and EVs by Illumina sequencing.  miRNAs that are significantly altered by Rab27a knockdown (KD) or miR-122 knockout (KO) are identified by comparing to the control cells (CTRL).

overall_design: EVs were collected by ultracentrifugation of the conditioned medium of MDA-MB-231-derived cells.  Cell RNA was extracted using TRIZOL, whereas EV RNA was extracted using TRIZOL LS (Thermo Fisher Scientific), and subjected to library construction and Illumina sequencing.

first: Shizhen

middle: E

last: Wang


title: Single-cell RNA sequencing of Smek1-/- cortices and hippocampus

first: Ruonan

last: Duan

address: 44# Wen Hua Xi Road

institute: Shandong University

summary: PPP4R3A, namely SMEK1 (Suppressor of Mek1 null), encodes a regulatory subunit of protein phosphatase 4 that is highly expressed in nervous system. Experimental autoimmune encephalomyelitis (EAE) is an animal disease model of multiple sclerosis (MS) that involves the immune system and central nervous system (CNS). However, it is unclear how genetic predispositions promote neuroinflammation in MS and EAE. Here, we investigated how partial loss-of-function of suppressor of SMEK1facilitates the onset of MS and EAE. Smek1 deficient mice showed more severe symptoms after EAE immunization. We performed single-cell RNA sequencing (scRNA-seq) on the cortices and hippocampus from 2-month old Smek1-/- and wild type littermates. Twelve cell types were identified in 6 tissue samples. Addtionally, we found a unique microglia subtype in Smek1-/- CNS that highly express IL-1β. Further analysis revealed enrichment of macrophage Csf1 in the novel microglia cluster. These findings confirmed that with loss of function of Smek1, a novel Csf1+ microglial cluster had a preactivated phenotype that may promote neuroinflammation.

overall_design: Four samples of cortices and hippocampus from 2-month old wild type (WT) and Smek1-/- mice

first: Ai

last: Liu

first: Anran

first: Qiji


title: RNA-seq analysis with isolated human pancreatic islets treated with human breast cancer cell secreted Evs or control

city: San Diego

first: Minghui

last: Cao

state: California

address: 9500 Gilman Dr

department: Pathology

institute: UC San Diego

summary: Epidemiological evidence has identified an association between breast cancer (BC) and systemic dysregulation of glucose metabolism. However, how BC influences glucose homeostasis remains unknown. Here we show that BC-derived extracellular vesicles (EVs) suppress pancreatic endocrine secretion to systemically reset glucose homeostasis. In pancreatic β-cells, miR-122 delivered in BC-derived EVs targets PKM to suppress glycolysis and ATP-dependent insulin exocytosis. Mice receiving high-miR-122 EVs or bearing BC xenograft tumors, but not those with tumors deficient in EV secretion or miR-122, exhibit suppressed insulin secretion, enhanced endogenous glucose production, impaired glucose tolerance, and hyperglycemia. Compared to non-cancer controls, BC patients have higher levels of EV-encapsulated miR-122 and fasting glucose but lower insulin levels in blood; the miR-122 levels are positively associated with glucose and negatively associated with insulin. This EV-mediated glucose reallocation at the whole-body level may contribute to tumor growth and progression, as well as higher incidence of diabetes in BC patients.

overall_design: Human pancreatic islets were isolated from non-diabetic human subjects and purchased from Lonza, California. PBS, Evs secreted from human breast cancer cell line MDA-MB-231 or from non-tumorigenic epithelial cells MCF-10A was added into cultured human pancreatic islets every 24 hours for twice. For each treatment, duplicates were included. Total RNA was extracted 24 hours after the second treatment and used for RNA-seq done by Novogene company.


title: Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci [RNA-seq]

city: Chapel Hill

first: Karen

middle: L

last: Mohlke

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: Chromatin accessibility and gene expression in relevant cell contexts can guide identification of regulatory elements and mechanisms at genome-wide association study (GWAS) loci. To identify regulatory elements that display differential activity across adipocyte differentiation, we performed ATAC-seq and RNA-seq in a cell model of preadipocytes and adipocytes at days 4 and 14 of differentiation. For comparison, we created a consensus map of ATAC-seq peaks in 11 subcutaneous adipose tissue samples. A set of 15,919 adipocyte-dependent peaks showed stronger enrichment (60.1%) of adipocyte nuclei enhancers than 51,855 adipose tissue peaks (44.6%) or 18,244 preadipocyte-dependent peaks (11.5%). We linked context-dependent peaks to genes based on adipocyte promoter capture Hi-C data, overlap with adipose eQTL variants, and differential gene expression. Of 16,167 context-dependent peaks that could be linked to a gene, 5,184 were linked by two or more strategies to 1,675 genes. Among GWAS loci for cardiometabolic traits, adipocyte peaks showed the strongest enrichment for waist-to-hip ratio, coronary artery disease, and HDL-cholesterol, while adipose tissue peaks also showed significant enrichment for LDL-cholesterol and triglyceride levels. We identified 666 peaks linked to 507 genes by two or more methods and overlapping a GWAS signal, suggesting a regulatory mechanism at these loci. At one GWAS locus for palmitoleic acid, rs603424 was located in an adipocyte-dependent peak linked to SCD and exhibited allelic differences in transcriptional activity in adipocytes (P=0.003) but not preadipocytes (P=0.09). These results demonstrate that context-dependent peaks and genes can guide discovery of regulatory variants at GWAS loci and aid identification of regulatory mechanisms.

overall_design: RNA-seq on SGBS preadipocytes and adipocytes at days 0, 2, 4, and 14 of differentiation

first: Hannah

middle: J

last: Perrin

first: Kevin

middle: W

last: Currin

first: Swarooparani

last: Vadlamudi

first: Gautam

middle: K

last: Pandey

first: Kenneth

last: Ng

first: Martin

last: Wabitsch

first: Markku

last: Laakso

first: Michael

middle: I

last: Love


title: A protective role for eosinophils in host resistance to Mycobacterium tuberculosis

city: Salvador

first: Artur

middle: Trancoso Lopo

last: Queiroz

address: Rua Waldemar Falcão, 121

country: Brazil

institute: Instituto Gonçalo Moniz

summary: Host resistance to Mycobacterium tuberculosis (Mtb) infection requires the activities of multiple leukocyte subsets, yet the roles of the different innate effector cells during tuberculosis (TB) are incompletely understood. Here we show a role for eosinophils in host resistance to Mtb infection. In humans, eosinophils are found in resected human TB lung lesions and autopsy granulomas. Eosinophils are also found in granulomas in zebrafish, mice, and non-human primates, where they are functionally activated and degranulate. Transcriptional profiling of lung tissue after Mtb infection of mice, that selectively lack eosinophils, revealed changes in neuronal associated pathways. Importantly, employing several independent models of eosinophil deficiency in mice, we demonstrate that eosinophils are required for optimal pulmonary bacterial control and host survival after Mtb infection. Collectively, our findings establish an unexpected role for eosinophils, granulocytes typically associated with type II inflammation, in host resistance against Mtb, a major human bacterial pathogen.

overall_design: 18 C57BL/6 mouses with and without eosinophils were infected with TB

first: Andrea

last: Bohrer

first: Ehydel

last: Castro

first: Zhidong

last: Hu

middle: T

first: Claire

last: Tocheny

first: Maike

last: Assmann

first: Shunsuke

last: Sakai

first: Christine

last: Nelson

first: Paul

last: Baker

first: Hui

last: Ma

first: Lin

first: Wen

last: Zilu

first: Elsa

last: du Bruyn

first: Catherine

last: Riou

first: Keith

middle: D

last: Kauffman

first: Ian

middle: N

last: Moore

first: Franca

last: Del Nonno

first: Linda

last: Petrone

first: Delia

last: Goletti

first: Mark

last: Cronan

first: Robert

last: Wilkinson

first: Clifton

last: Barry III

first: Laura

last: Via

first: Daniel

last: Barber

first: Amy

last: Klion

first: Bruno

middle: B

last: Andrade

first: Yanzheng

last: Song

first: Ka-Wing

last: Wong

first: Katrin

last: Mayer-Barber


title: HFSF co-cultured with blue light exposed RPE medium

city: Shanghai

first: Gu

last: Ping

address: Manufacturing Road, 833

department: Department of Ophthalmology

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

summary: we use bluel light exposed RPE medium to cultured HFSF

first: Xiaochan

last: Dai


title: Single cell transcriptomics of cardiac immune cells after pressure overload

city: Minneapolis

first: Adam

last: Herman

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

summary: Cardiac immune cells play important roles in orchestrating the response of the heart to stress and injury. The precise role of immune cells in the early phase after cardiac pressure overload is unclear. Clustering analysis of >33,000 sequenced single cells identified 25 immune cell populations including 12 macrophage and monocyte populations.

overall_design: Mice were subjected to sham or TAC surgeries, followed by cardiac non-cardiomyocyte isolation 1 week later. Immune cells were enriched by magnetic selection, followed by barcoded antibody incubation to allow identification of 4 sham and 6 TAC samples after 10x Genomics droplet sequencing.

first: Xavier

middle: S

last: Revelo

first: Preethy

last: Parthiban

first: Chen

last: Chen

first: Fanta

last: Barrow

first: Gavin

last: Fredrickson

first: Haiguang

last: Wang

first: Doğacan

last: Yücel

first: Jop

middle: H

last: van Berlo


title: miRNA sequencing of circCpsf6 silencing models in N2A cells

city: Shenzhen

first: Changrui

last: Tie

institute: Shenzhen Medical Center

summary: To search and identify the potential downstream miRNAs of circCpsf6, miRNA sequencing analysis was performed on circCpsf6 silencing models in N2A cells. The differential expression of miRNAs caused by the knockdown of circCpsf6 was revealed in the volcano plot.Heatmaps indicated the upregulated and downregulated clusters of differential miRNAs in N2A cells when circCpsf6 was silenced.

overall_design: MiRNAs profiles of si-NC and si-circCpsf6 in N2A cells


title: circCpsf6 silencing models in N2A cells

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: mRNA sequencing of circCpsf6 silencing models in N2A cells

summary: mRNA sequencing was performed to  explore involved mRNAs when circCpsf6 was silenced in N2A cells.The differential expression of mRNAs caused by the knockdown of circCpsf6 was revealed in the volcano plot.Heatmaps indicated the upregulated and downregulated clusters of differential mRNAs when circCpsf6 was silenced in N2A cells

overall_design: mRNAs profiles of si-NC and si-circCpsf6 in N2A cells


title: Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci [ATAC-seq]

first: Karen

last: Mohlke

overall_design:
ATAC-seq on SGBS preadipocytes and adipocytes at days 0, 2, 4, and 14 of differentiation and bulk adipose tissue from 17 individuals
**Please note that the 'adiposeTissue' raw data require controlled access and thus are not provided****

first: Hannah

last: Perrin

first: Kevin

last: Currin

first: Swarooparani

last: Vadlamudi

first: Gautam

last: Pandey

first: Kenneth

last: Ng

first: Martin

last: Wabitsch

first: Markku

last: Laakso

first: Michael

last: Love


title: Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci


title: Temporal profile of brain gene expression associated with learning in an anuran amphibian II

city: Ottawa

first: Vern

last: Lewis

state: Ontario

address: 1125 Colonel By Drive

department: Neuroscience

country: Canada

institute: Carleton University

summary: Reported here are the transcriptomic changes resulting from extinction learning, in the brain of an anuran amphibian. RNA sequencing was utilized to investigate gene expression patterns resulting from conditioned learning in the fire-bellied toad, Bombina orientalis. As a basal tetrapod lineage, B. orientalis represents a robust candidate for investigating the evolution of molecular mechanisms underlying learning in vertebrates. The gene expression patterns associated with extinction learning in this species shared similarities with to those found in mammals submitted to extinction, but interesting divergent profiles highlighted potential differences in the mechanisms of learning and memory among tetrapods.

overall_design: Experiment consisted of four treatments with three replicates each. Treatments represent training type (Short vs. Long) and post-training sacrifice timing (2 hours & 24 hours; n=12). For the resulting trancriptome assembly, these 12 samples were combined with the 2h & 24h (n=6) datasets from our previous RNA-seq exeriment. GEO submission: GSE135054.

first: Frederic

last: Laberge

first: Andreas

last: Heyland


title: ERYTHROID MITOCHONDRIAL RETENTION TRIGGERS MYELOID-DEPENDENT TYPE I INTERFERON IN HUMAN SLE

city: Dallas

first: Uthra

last: Balaji

address: 3434 Live Oak St

department: Biostatistics Core

institute: Baylor Scott & White Research Institute

summary: Using both in vitro-derived RBCs as well as RBCs isolated from SLE and CANDLE patients we were able to demonstrate that a defective proteasome activation during human erythropoiesis leads to the generation of pro-inflammatory RBCs that retain mitochondria.

overall_design:
RNA-seq of PBMC from SLE patients and RBCs derived from PBMC from healthy donors and SLE patients.

RBC group definitions:
Mito- RBCs group are PBMCs from SLE patients that do not carry mitochondria inside their RBCs (Red blood cells)
Mito+ RBCs : Ops IgG- group are PBMCs from SLE patients that carry mitochondria inside their RBCs (Red blood cells) and they don't have opsonizing anti-RBCs IgG in their plasma
Mito+ RBCs : Ops IgG+ group are PBMCs from SLE patients that carry mitochondria inside their RBCs (Red blood cells) and they have opsonizing anti-RBCs IgG in their plasma

first: Simone

last: Caielli

first: Jacob

last: Cardenas

first: Adriana

last: Almeida de Jesus

first: Jeanine

last: Baisch

first: Lynnette

last: Walters

first: Jean

middle: P

last: Blanck

first: Preetha

last: Balasubramanian

first: Cristy

last: Stagnar

first: Marina

last: Ohouo

first: Seunghee

last: Hong

first: Marilynn

last: Punaro

first: Lorien

last: Nassi

first: Katie

last: Stewart

first: Julie

last: Fuller

first: Jinghua

last: Gu

first: Jacques

last: Banchereau

first: Tracey

last: Wright

first: Raphaela

last: Goldbach-Mansky

first: Virginia

last: Pascual


title: DNA copy number alterations in radiation-induced rat mammary carcinomas

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

institute: National Institutes for Quantum and Radiological Science and Technology

summary: To investigate DNA copy number changes in rat mammary carcinomas induced by ioizing radiation.

overall_design: DNA copy number changes in radiation-induced rat mammary carcinomas were analyzed using array-CGH microarray.

first: Mayumi

last: Nishimura

last: Daino

first: Atsuko

last: Ishikawa

first: Tatsuhiko

last: Imaoka


title: Expression data from 3-month-old mouse hippocampus of Ts1Cje and wild-type mice

city: Kyoto

first: Keiichi

last: Ishihara

state: Kyoto

address: 5 Misasagi Nakauchi-cho, Yamashina-ku

department: Department of Pathological Biochemistry

institute: Kyoto Pharmaceutical University

summary: The Ts1Cje mouse model of Down syndrome (DS) has partial triplication of mouse chromosome 16, of which a large portion is homologous to human chromosome 21. The mouse model shows an impaired neurogenesis in hippocampus at 3-month-old . We analyzed the effect of Ts1Cje trisomic region on global gene expression in the adult brain of Ts1Cje mice at 3-month-old.

overall_design: RNA was extracted from hippocampus for hybridization to arrays from 4 pairs of Ts1Cje and disomic wild-type littermate control.


title: Epigenetically regulated transcription factor network of intestinal M cell differentiation

city: Tampere

first: Mikko

last: Oittinen

address: Arvo Ylpön katu 34

department: Tampere Center for Child Health Research

country: Finland

institute: Tampere University

summary: Stem cells derived from mouse intestine were differentiated to M-cells using RANKL treatment in an organoid culture system. PRC2 controlled differentiation was studied with H3K27me3 ChIP-Seq and GRO-Seq.

overall_design: Differential GRO-Seq and ChIP-Seq (H3K27me3) was performed on mouse mini-gut model cells.

first: Joel

last: Jonhson

first: Keijo

last: Viiri


title: Profiles of mRNA and lncRNA expression in colorectal cancer

city: Dongguan

first: Guangxian

last: Xu

state: Guangdong

address: No.1 Xincheng Blvd, Songshan Lake National High-tech Industrial Development Zone

department: College of Medical Technology

institute: Guangdong Medical University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Colorectal cancer (CRC) is one of the most malignant cancers with high morbidity and mortality. Genetic factors are involved in the carcinogenesis of CRC, which consists of a complex accumulation of mutations in key regulatory genes and epigenetic regulation.Here we report significantly up-regulated as well as down-regulated mRNAs and lncRNAs in CRC tissues compared with their matched non-tumoral tissues.

overall_design: Examination of  Differential Expression of mRNAs and lncRNAs between 3 pairs of colorectal tumor tissues and normal tissues

first: Dan

last: Jiang


title: Expression profiling of WT and Dot1L KO CD8 effector T cells and H3K79me2 occupancy in WT effector CD8 T cells

city: Amsterdam

first: Fred

last: van Leeuwen

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

summary: We studied the role of the histone methyltransferase DOT1L in T cell development and differentiation. We generated RNA-seq data from sorted CD8 effector T cells from WT (Lck-cre+/-) and Dot1L KO (Lck-cre+/-;Dot1Lfl/fl) mice infected with Listeria monocytogenes. This data was compared with H3K79me2 ChIP-seq data from the same T cell subset.

overall_design: RNA-seq and H3K79me2 ChIP-seq of sorted CD8 effector T cells from WT and Dot1L KO mice infected with Listeria.

first: Teun

middle: A

last: van den Brand

first: Eliza

middle: M

last: Kwesi-Maliepaard

first: F


title: LAMP5-AS1 drives leukemia cell stemness in MLL leukemia

city: Guangzhou

first: Wen-Tao

last: Wang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: sun yat sen university

summary: Mixed lineage leukemia (MLL) gene rearrangements trigger aberrant epigenetic modification and gene expression in hematopoietic stem and progenitor cells, which generates one of the most aggressive subtypes of leukemia with an apex self-renewal. It remains a challenge to directly inhibit rearranged MLL itself because of its multiple fusion partners and the poorly annotated downstream genes of MLL fusion proteins; therefore, novel therapeutic targets are urgently needed. We discovered that a long noncoding RNA (lncRNA) LAMP5-AS1 can promote higher degrees of H3K79 methylation, followed by upregulated expression of the self-renewal genes in the HOXA cluster, which are responsible for leukemia stemness in context of MLL rearrangements. Mechanistically, LAMP5-AS1 facilitated the methyltransferase activity of DOT1L by directly binding its Lys-rich region of catalytic domain, thus promoting the global patterns of H3K79 dimethylation and trimethylation in cells. These observations supported that LAMP5-AS1 upregulated H3K79me2/me3 and the transcription of DOT1L ectopic target genes. This is the first study that a lncRNA regulates the self-renewal program and differentiation block in MLL leukemia cells by facilitating the methyltransferase activity of DOT1L and global H3K79 methylation, showing its potential as a therapeutic target for MLL leukemia.

overall_design: ShNC and shLAMP5-AS1 MOLM-13 cells used

first: Yue-Qin

last: Chen

first: Yu-Meng

last: Sun


title: miRNA, mRNA and lncRNA expression in colorectal cancer

type:
Non-coding RNA profiling by array
Expression profiling by array


title: Evaluation of commercially available small RNA methods for plant samples

city: Davis

first: Patricia

last: Baldrich Gonzalez

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

summary: Plant small RNAs are a diverse and complex set of molecules, ranging in length from 21 to 24 nt, involved in a wide range of essential biological processes. Nowadays, high-throughput sequencing is the most commonly used method for the discovery and quantification of small RNAs. However, it is known that several biases can occur during the preparation of small RNA libraries, especially using low input RNA. We used two types of plant biological samples to evaluate the performance of seven commercially available methods for small RNA library construction, using different RNA input amounts. We show that when working with plant material, library construction methods have differing capabilities to capture small RNAs, and that different library construction methods provide better results when applied to the detection of microRNAs, phased small RNAs, or tRNA-derived fragments.

overall_design: In this study we include 96 small RNAseq samples, made with seven different commercially available kits, two types of RNA samples ( pre-meiotic and meiotic anthers from maize) and four different RNA input amounts (1000ng, 100ng, 10ng and 1ng). All the samples include three technical replicates.

last: Baldrich

first: Saleh

last: Tamim

first: Sandra

last: Mathioni

first: Blake

last: Meyers


title: Differentially expressed miRNAs in colorectal cancer

summary: Colorectal cancer (CRC) is one of the most malignant cancers with high morbidity and mortality. MicroRNAs (miRNAs) are small noncoding RNAs that affect biological processes by binding to mRNAs and regulating their expression, and epigenetic alterations including miRNA dysregulation are significantly involved in CRC development. Here we report significantly up-regulated as well as down-regulated miRNAs in CRC tissues compared with their matched non-tumoral tissues.

overall_design: Examination of  Differential expression of miRNAs between 3 pairs of colorectal tumor tissues and normal tissues


title: RNA-seq analysis for mRNA expression difference between male and female cultured oligodendrocyte precursor cells

city: Kobe

first: Yuichi

last: Ono

state: Hyogo

address: 6-8-2 Minatojima-minamimachi, Chuo-ku

department: Developmental Neurobiology

institute: KAN Research Institute Inc.

summary: The susceptibility to neurological and psychiatric disorders reveals sex-specific differences. Several studies have reported sex-related differences in the structure and function of human brains. Oligodendrocyte precursor cells (OPCs) regulate the neuronal system in various ways and play crucial roles in brain homeostasis besides their well-known role as a reservoir for mature oligodendrocytes. Here, we revealed transcriptomic differences in OPCs isolated from male and female neonatal rat brains.

overall_design: mRNA profiles of primary cultured  oligodendrocyte precursor cells derived from male and female neonatal rats were generated by deep sequencing, in quadruplicate, using Illumina MiSeq.

first: Ken

last: Yasuda

first: Takakuni

last: Maki

first: Yusuke

last: Kinoshita

first: Ryosuke

last: Takahashi


title: Gut microbiome dysregulation is associated with elevated toxic bile acids in Parkinson’s disease

city: Grand Rapids

first: Peipei

last: Li

state: MI

address: 333 Bostwick Ave N.E.

department: Center for Neurodegenerative Science

institute: Van Andel Research Institute

summary: The gut microbiome can impact brain health and is altered in Parkinson’s disease (PD) patients. The vermiform appendix is a lymphoid tissue implicated in the storage and regulation of the gut microbiome. Here, we investigate changes in the functional microbiome in the appendix of PD patients relative to controls by metatranscriptomic analysis. In the PD appendix, we find microbial dysbiosis affecting lipid metabolism, particularly an upregulation of bacteria responsible for secondary bile acid synthesis. Likewise, proteomic and transcript analysis in the PD gut corroborates a disruption in cholesterol homeostasis and lipid catabolism. Bile acid analysis in the PD appendix reveals an increase in the microbially-derived, toxic secondary bile acids deoxycholic acid (DCA) and lithocholic acid (LCA). Synucleinopathy in mice induces similar microbiome alterations to those of PD patients and heightens microbial changes to gut inflammation. As observed in PD, the mouse model of synucleinopathy has elevated DCA and LCA. Raised levels of DCA and LCA can lead to liver injury, and an analysis of blood markers of liver dysfunction shows evidence of biliary abnormalities in PD patients, including elevated alkaline phosphatase and bilirubin. Increased bilirubin levels are also evident before PD diagnosis, in individuals at-risk of developing PD. In sum, microbially-derived toxic bile acids are heightened in PD and biliary changes may even precede the onset of overt motor symptoms.

overall_design: The cecal patch microbiome was profiled in a mouse model of synucleinopathy as well as in response to gut inflammation. We examined microbiome changes by 16S rRNA sequencing of the V3-V4 hypervariable region. Microbiome changes were profiled in wild-type mice and in the synucleinopathy model: hemizygous Tg(Thy1-SNCA*A30P)18Pjk mice (A30P α-syn), which overexpress human α-syn with the A30P mutation under the neuron-selective Thy1 promoter. A30P α-syn mice have been maintained on a C57BL/6 background for over 10 generations. Gut inflammation was induced using dextran sodium sulfate (DSS), a widely used model of ulcerative colitis. Adult wild-type and A30P α-syn mice (3-months of age) were exposed to a chronic DSS protocol that began at DSS concentration of 2.5% and increased to 4% over 4 cycles (+0.5% increment per cycle). One cycle consisted of 5 days of DSS, followed by 2 days of water (DSS: 160110, MP Biomedicals, LLC). The non-DSS colitis groups were administered normal drinking water. Mice were then given a 4-week-long recovery period during which they received normal drinking water, followed by tissue harvest.

first: Bryan

last: Killinger

first: Ian

last: Beddows

first: Elizabeth

last: Ensink

first: Ali

last: Yilmaz

first: Noah

last: Lubben

first: Jared

last: Lamp

first: Meghan

last: Schithuis

first: Irving

last: Vega

first: Markus

last: Britschgi

first: Andrew

last: Pospisilik

first: Patrik

last: Brundin

first: Lena

first: Stewart

last: Graham

first: Viviane

last: Labrie


title: Comparison of periosteal, adipose, and dermal CD146+ human pericytes

city: Baltimore

first: Aaron

last: James

address: 600 North Wolfe Street

institute: Johns Hopkins University School of Medicine

summary:
Human pericytes demonstrate multilineage differentiation potential, and their descendants participate in tissue homeostasis and repair.  Increasing evidence from developmental biology and tissue engineering suggest that regional specification by tissue of origin exists among human pericytes.  Here, we sought to define the differentiation of CD146+ human pericytes from skeletal and soft tissue sources.  Uncultured CD146+CD31-CD45- pericytes were derived by fluorescent activated cell sorting from human periosteum, adipose, or dermal tissue.  Periosteal CD146+CD31-CD45- cells retained canonical features of pericytes, including cell surface marker expression, multilineage differentiation potential, and paracrine induced tubulogenesis.  Periosteal pericytes demonstrated a striking tendency to undergo osteoblastogenesis, while soft tissue pericytes did not in vitro or in vivo.  Microarray analysis demonstrated substantive differences between periosteal pericytes in comparison to their soft tissue pericyte counterparts.  In sum, skeletal and soft tissue pericytes differ in their relative lineage differentiation potential and ability to form bone.
Human tissues were microdissected, digested, and FACS sorted to derived a CD146+CD31-CD45- pericyte population, and cells were expanded in standard growth medium (DMEM, 10% FBS, 1% pen/strep) and nucleic acid isolated at subconfluency

overall_design: Human periosteum, subcutaneous adipose tissue, or dermis was obtained from human tissues (n=3 biologic replicates per site, 9 total), enzymatically digested, and a CD146+CD31-CD45- pericyte population was purified by fluorescent activated cell sorting. Cells were expanded at 37°C in a humidified atmosphere containing 95% air and 5% CO2.  All cells were cultured in DMEM medium with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.  Medium was changed every three d, and nucleic acid was harvested at subconfluency.

first: Jiajia

last: Xu


title: C. elegans PPM-2 regulates small RNA function by stabilizing Argonaute proteins

city: Riverside

first: Weifeng

last: Gu

address: 900 University Ave

department: Molecular, Cell and Systems Biology

institute: University of California at Riverside

summary: Argonaute proteins associate with small non-coding RNAs such as microRNAs, piRNAs and siRNAs to regulate gene expression required for cell proliferation and differentiation. Thse Argonaute proteins are the major components of effector complexes of non-coding RNA pathways. In C. elegans, we identified PPM-2, a Mg2+/Mn2+-dependent serine/threonine phosphatase, as a new regulator of the small RNA pathways in C. elegans. We demonstrate that PPM-2 is involved in the regulation of the let-7 microRNA family but also in the regulation of nuclear RNAi as well as it contributes to the expression of piRNAs. The loss of ppm-2 affects the expression level of Type 1 piRNAs and the stability of ALG-1, PRG-1 and NRDE-3 Argonaute proteins by sending them to the proteasomal degradation pathway. Altogether, our findings suggest that PPM-2 is regulating the function of small non-coding RNA pathways by preventing Argonaute proteins to be degraded via the proteasomal pathway.

overall_design: Develop a novel protocol to clone small RNA and mRNA

first: Lucile

last: Fressigné

first: Francois

last: Houle

first: Gabriel

last: Bossé

first: Lichao

first: Guillaume

last: Proulx-Landry

first: Martin

last: Simard


title: A Quantitative Sequencing Method for 5-Formylcytosine in RNA

city: Chicago

first: Ruitu

last: Lyu

state: IL

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

summary: 5-Formylcytosine (f5C) modification is present in human mitochondrial methionine tRNA (mt-tRNAMet) and cytosolic leucine tRNA (ct-tRNALeu), with their formation mediated by NSUN3 and ALKBH1. f5C has also been detected in mRNA of yeast and human cells, but its transcriptome-wide distribution has not been studied. Here we report f5C-seq, a quantitative sequencing method to map f5C transcriptome-wide in HeLa and mouse embryonic stem cells (mESCs). We show that f5C in RNA can be reduced to dihydrouracil (DHU) by pico-brane, and DHU can be exclusively read as U during reverse transcription (RT) reaction, allowing the detection and quantification of f5C sites by a unique C-to-U mutation signature. We validated f5C-seq by identifying and quantifying the two known f5C sites in tRNA, in which the f5C modification fractions dropped significantly in ALKBH1-depleted cells. By applying f5C-seq to small RNA, we identified 13 and 11 new f5C sites in HeLa and mESC tRNA, respectively.

sample_organism:
Homo sapiens
Mus musculus
synthetic construct

overall_design: We developped a quantitative sequencing method to map f5C transcriptome-wide in HeLa and mouse embryonic stem cells (mESCs).

first: Qing

last: Dai

first: Chuan

last: He


title: The role of HHIP in COPD lymphocytic inflammation

city: Boston

first: Jeong

last: Yun

state: MA

address: 181 Longwood Ave

institute: BRIGHAM AND WOMEN'S HOSPITAL

summary:
Chronic obstructive pulmonary disease (COPD) is characterized by persistent and amplified inflammation to cigarette smoke in vulnerable subjects. The genetic risk of persistent inflammation is poorly understood. A mouse model targeting hedgehog interacting protein (HHIP)(Hhip+--), a genetic risk factor for COPD, displays progressive, persistent inflammation resembling human cases, providing a valuable model to study the contribution of the genetic risk factor HHIP to inflammation in COPD.
By single cell RNA sequencing of Hhip+-- lungs at different disease stages, we identified induction of IFN-gamma in activated CD8+T cells possibly driving the inflammatory phenotype in Hhip+-- lungs. Hhip expression was restricted to lung fibroblasts, which interaction with CD8+T cells were mediated by increased levels of IL-18 from Hhip+-- fibroblasts.  Our finding provides insight into how a common genetic variation contributes to the amplified lymphocytic inflammation in COPD.

overall_design: single cell RNA sequencing of Hhip+-- and Hhip+-+ mouse lungs at 4 different age points

first: Xiaobo

last: Zhou


title: Transcriptomic analysis of HeLa cells depleted in CELF1, ELAVL1, and both

city: Rennes

first: Luc

last: Paillard

address: 2 Ave Leon Bernard

country: France

institute: Univ Rennes

summary: ELAVL1 and CELF1 are two RNA-binding proteins involved in alternative splicing control. To address their functional relationships, we identify the differentially spliced mRNAs upon depletion of CELF1, ELAVL1, or both. These proteins control similar sets of genes with similar consequences on exon inclusion or skipping. The magnitude of the effect of the double depletion equals the sum of the magnitudes of the individual depletions, showing that CELF1 and ELAVL1 additively control their target RNAs. CELF1 and ELAVL1 regulated splicing events  include ACSL4, WNK1, CD44, MICAL3, and JDP2. Using FRET, we find that CELF1 and ELAVL1 directly interact in cell nuclei. We demonstrate that the combined levels of CELF1 and ELAVL1 is a valuable biomarker in breast cancer, while their levels bring very limited information when taken individually. A “co-RNA splicing map” of CELF1 and ELAVL1 shows they repress alternative splice sites when bound nearby, but activate them when bound further away. Together, these data point to strong functional interactions between CELF1 and ELAVL1 to control alternative splicing with significant impacts in human pathology.

overall_design: HeLa cells were transfected with mock siRNAs, or siRNAs directed against CELF1, ELAVL1, or both. RNAs were extracted 48h after siRNA transfection. Three independent transfection experiments were carried out for each depletion (II, III, IV). Please note that there are 6 raw files for 12 samples since two samples were on the same array, one in Cy3 and one in Cy5. The corresponding raw data file for each sample is indicated in the Sample description field.

first: Géraldine

last: David

first: Stéphane

last: Deschamps

first: Yann

last: Audic


title: Global examination of H3K9me3 levels and PEG3 binding sites between WT and KO

status: Public on Jul 31 2021

city: Baton Rouge

first: Joomyeong

last: Kim

state: LA

address: 202 Life Sciences Bldg

department: Biological Sciences

institute: Louisiana State University

summary: PEG3 (Paternally Expressed Gene 3) is an imprinted gene encoding a DNA-binding protein. In this study, we used MEF cells (Mouse Embryonic Fibroblast). We performed genome-wide ChIP-seq experiments profiling H3K9me3 levels as well as examine the set of genomic targets and also redefines the DNA-binding motif for the imprinted transcription factor, PEG3 in the WT and KO of Peg3. The results suggested high levels of H3K9 levels in Peg3-KO MEFs than in Peg3-WT MEFs, whereas several different genes involved several biochemical pathways seems to be have potential binding site for PEG3 protein, which tend to have a distinct profile of binding motif to its binding region. This further suggests that mammalian Peg3 may control its downstream genes in regulating several biological functions and regulate the H3K9 methylation levels.

overall_design: Assessing histone profiles and binding site of Peg3 in two different 14.5 days old wild type (WT) and knockout (KO) mouse embryonic fibroblast cells

first: J

first: S

last: Ghimire


title: Co-infection wtih porcine reproductive and respiratory syndrome virus (PRRSV) and M. hyopneumoniae (Mhp) enhances pathogenicity  by upregulation of inflammatory response in piglets

city: Nanjing

first: Bin

last: Li

state: Jiangsu

address: 50# Zhongling Street

department: Institute of Veterinary Medicine

institute: Jiangsu Academy of Agricultural Sciences

summary:
To investigate the  gene expression level changes in the whole genome scale in porcine alveolar macrophage collected from the piglets  individually or dually infected with  PRRSV and Mph
The results in this study will be further described in Bin li et al., 2021. Veterinary microbiology

overall_design: A 24 chip study using total RNA recovered from four separate group include control, PRRSV, Mph and PRRSV+Mph


title: Cappable-Seq analysis of the N. punctiforme primary transcriptome during hormogonium development in wild type, and three sigma-factor deletion strains

city: Stockton

first: Douglas

last: Risser

address: 3601 Pacific Ave

department: Biology

institute: University of the Pacific

summary: Cappable-Seq  (Ettwiller et. al., BMC Genomics volume 17, Article number: 199 (2016)) was employed to identify transcriptional start sites (TSSs) representing the primary transcriptome of hormogonia, motile filaments of the filamentous cyanobacterium in N. punctiforme ATCC29133. TSSs were defined using the wild-type strain and subsequently the expression of these TSSs was analyzed in each of three sigma-factor deletion mutant strains.

overall_design: Total RNA from a single biological replicate at 6 hours after hormogonium induction from either the wild-type strain, or sigJ (UOP132), sigC (UOP131), and sigF (UOP141) mutant strains (Gonzalez et. al., mSphere 4(3) 2019) was used to prepare cDNA libraries for Cappable-Seq as described by (Ettwiller et. al., BMC Genomics volume 17, Article number: 199 (2016)), apended with adapters and single-read sequenced in 1 lane of a flow cell on an Illumina NextSeq 500 system using 75 bp read length


title: Transcriptome Profile Analysis Reveals the Regulation Mechanism of Stamen Abortion in Handeliodendron bodinieri（Levl.）Rehd

city: nanning

first: tianfeng

last: liu

address: Xixiangtang Street

institute: guangxi university

summary: To elucidate the molecular mechanism of stamen abortion underlying sex differentiation from transcriptomic aspects in Handeliodendron bodinieri, we use abnormal stamens before and after abortion in female flowers and normal stamen in male flowers at the same stage as control material. Key genes regulating stamen abortion was identified by using RNA-seq technique. The results show that it was abortion science stage 6 during anther development, at the same time, HbGPAT, HbAMS, HbLAP5, HbLAP3 and HbTES were down-regulated , and HbML5 was up-regulated. Therefore, these information will provide theoretical foundation for the conservation, breeding, scientific research and application of Handeliodendron bodinieri.

overall_design: Flower buds and anthers mRNA profiles of  male and female flowers in Handeliodendron bodinieri（Levl.）Rehd

first: Tianfeng

last: Liu

first: Xiatong

first: Chong

last: Zhang

first: Xiaorui

last: Guo

first: Hui

first: Song

first: Zailiu

first: Hai

last: Lu


title: Thirty-eight-negative-kinase 1 (TNK1) is a major mediator of trauma induced intestinal injury and multi-organ failure

city: Ulm

first: Hans

last: Kestler

address: Albert-Einstein-Allee 11

department: Research Group Bioinformatics and Systems Biology

institute: University of Ulm

summary: To check gene expression signatures in response to TNK1 expressionin intestine, we performed whole genome microarray on intestinal (ileum) epithelial cells purified from TNK1 expressing and not expressing mice

overall_design: Inducible TNK-knockin mice (Rosa26rtTA/+, Hprt Myc-Tnk1tg)  were treated with doxycyline for 24h to induce TNK1 expression in the gut. TNK-knockin mice treated  with the saline solution under the same experimental conditions served as control cohort.


title: Development of a Classification Taxonomy for Adipogenic Chemicals: A Novel Tool for Identifying Emerging Metabolic Health Threats

city: Medford

first: Eric

middle: R

last: Reed

address: 419 Boston Ave.

department: Data Intensive Studies Center

institute: Tufts University

summary: Growing evidence suggests that chemicals in disparate structural classes activate specific subsets of PPARγ’s transcriptional programs to generate adipocytes with distinct phenotypes. Our objectives were to 1) establish a novel classification method to predict PPARγ-interacting and modifying chemicals and 2) create taxonomy labels to group chemicals based on their effects on PPARγ’s transcriptome and downstream metabolic functions. We tested the hypothesis that an environmental ligand highly ranked by the taxonomy, but that segregated from the therapeutic ligands, would induce white but not brite adipogensis. 3T3-L1 cells were differentiated in the presence of 76 chemicals (negative controls, synthetic nuclear receptor ligands known to influence adipocyte biology, suspected environmental PPARγ ligands). Differentiation was assessed by measuring lipid accumulation. mRNA expression was determined by highly multiplexed RNA-Seq and validated by RT-qPCR. A novel classification model was developed using an amended random forest procedure. A subset of environmental contaminants identified as strong PPARγ agonists were characterized further for lipid handling, mitochondrial biogenesis and cellular respiration in 3T3-L1 cells and primary human preadipocytes. The 76 chemicals generated a spectrum of adipogenic differentiation. We used lipid accumulation and RNA sequencing data to develop a classification system that 1) identified PPARγ agonists and 2) sorted agonists into likely white or brite adipocyte inducers. Expression of Cidec, was the most efficacious indicator for strong PPARγ activation. Two known environmental PPARγ ligands, tetrabromobisphenol A, and triphenyl phosphate, which sorted distinctly from therapeutic ligands, induced white but not brite adipocyte genes and induced fatty acid uptake but not mitochondrial biogenesis in 3T3-L1 cells. The highly ranked agonists, tonalid and quinoxyfen, also induced white adipogenesis in 3T3-L1 cells and primary human preadipocytes. A novel classification procedure accurately identified environmental chemicals as PPARγ-modifying chemicals distinct from known PPARγ-modifying therapeutics.

overall_design: 3' Digital Gene Expression (3'DGE) for mature NIH 3T3-L1 folliwng exposure to a panel of compounds during differentiation.

first: Stephanie

first: Stephen

last: Farmer

first: Stefano

last: Monti

first: Jennifer

last: Schlezinger


title: Chromatin-mediated alternative splicing regulates cocaine reward behavior

city: Philadelphia

first: Song-Jun

last: Xu

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary:
Neuronal alternative splicing is a key gene regulatory mechanism in brain. Yet the spliceosome machinery is insufficient to fully specify splicing complexity. In considering the role of the epigenome in activity-dependent alternative splicing, we and others find the histone modification, H3K36me3, to be a putative splicing regulator. In the current study, we found that mouse cocaine self-administration caused widespread differential alternative splicing, concomitant with enrichment of H3K36me3 at differentially spliced junctions. Importantly, only targeted epigenetic editing can distinguish between a direct role of H3K36me3 in splicing and an indirect role via regulation of splice factor expression elsewhere on the genome. We targeted Srsf11, which was both alternatively spliced and H3K36me3 enriched in brain following cocaine self-administration.
Results: Epigenetic editing of H3K36me3 at Srsf11 was sufficient to drive its alternative splicing and enhanced cocaine self-administration, establishing the direct causal relevance of H3K36me3 to alternative splicing of Srsf11 and to reward behavior.

overall_design: H3K36me3 ChIP-seq identified H3K36me3 enrichment at splice junctions (N=3) in cocaine samples. H3K36me3 Cut&Run-seq (N=6) of dCas9-SET2-sgRNA transfected N2a cells confirmed increased H3K36me3 enrichment in Srsf11 splice junction. Alternative splicing analysis of dCas9-Set2-Srsf11 targeted NAc (N=4) identified its alternative splicing profile. H3K36me3 ChIP-seq (N=3) and RNA-seq (N=3) in HSV-Set2 transfected NAc assessed how H3K36me3 regulated alternative splicing globally in NAc.

first: Sonia

last: Lombroso

first: Delaney

last: Fischer

first: Marco

last: Carpenter

first: Dylan

last: Marchione

first: Peter

last: Hamilton

first: Carissa

last: Lim

first: Rachel

last: Neve

first: Benjamin

last: Garcia

first: Mathieu

middle: E

last: Wimmer

first: R

middle: C

last: Pierce

first: Elizabeth

last: Heller


title: Transcriptome analysis of Arabidopis seedlings grown on MS medium with and without ethanol

city: Yokohama

first: Akihiro

last: Matsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

institute: RIKEN

summary: To identify ethanol-induced genes, gene expression profile between arabidopis seedlings grown on MS medium with and without ethanol using the custom microarray (GPL22706) were analyzed.

overall_design: Arabidopsis thaliana wild type (Col-0) were sown on MS medium with and without 2 mM  ethanol. Then, the plants grown at 22  °C 16 h light / 8 h dark condition for 2 weeks were collected.

first: Yuji

last: Sunaoshi

first: Maho

last: Tanaka

first: Motoaki

last: Seki


title: RNA-seq Quantitative Analysis of Wild Type and Kcnh2-/- day4 cells derived from rESCs

city: Shanghai

first: Luying

last: Peng

state: Shanghai

address: 1239 Siping Road

department: School of Medicine

institute: Tongji University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. To understand how ERG1 executes its function during differentiation, we performed RNA-seq experiments in Kcnh2-/- and wild-type rEBs at day 4
Methods: RNA profiles of day 4  wild type (WT) and Kcnh2-/- rEBs were generated by deep sequencing, in duplicate, using Illumina Hiseq. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks.
Results: Using an optimized data analysis workflow, we mapped about 35 million sequence reads per sample to the rat genome (build mm9) and identified 16,014 transcripts in the retinas of WT and Kcnh2−/− rESC  with TopHat workflow. RNA-seq datashows 211 differentially expressed gene with a fold change ≥2 and p value <0.01, in which 109 genes were downregulated and 102 genes were upregulateds.Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method.Based on GO enrichment analysis results, the deletion of Kcnh2 resulted in the impaired heart development and cell differentiation by inhibiting the expression of heart related genes. KEGG enrichment analysis of all differentially expressed genes yielded the enrichment for several cell differentiation signaling pathways, like PI3K-Akt signaling pathway and Wnt signaling pathway, which is  consistent with the experiment results.
Conclusions: Our study represents the detailed analysis of transcriptomes of Kcnh2-/- vs. WT  rat embryonic stem cell, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: MRNA profiles of  day 4  wild type (WT) and Kcnh2-/- rEBs  were generated by deep sequencing, in duplicate, using Illumina Hiseq.

first: Duo

last: Wang

first: Yumei


title: The carP lncRNA is a carS-related regulatory element with broad effects on the Fusarium fujikuroi transcriptome

first: Javier

last: Avalos

address: Av. Reina Mercedes sn

department: Genetics

country: Spain

institute: University of Seville

summary: Carotenoid biosynthesis in the fungus Fusarium fujikuroi is regulated by environmental factors, with light as the main stimulating signal. The CarS RING finger protein plays an important role downregulating the structural genes of the carotenoid pathway. A recent transcriptomic analysis on the effect of carS mutation identified a gene for a lncRNA upstream of carS, called carP, whose deletion results in increased levels of carS mRNA and lack of carotenoid production. We have investigated the function of carP by studying the transcriptomic effect of its deletion and the phenotypes resulting from the reintroduction of carP to a deletion strain. RNA-seq data showed that the loss of carP affected the mRNA levels of hundreds of genes, especially after illumination. Many of these changes appeared to be cascade effects as a result of changes in carS expression, as suggested the comparison with differentially expressed genes in the carS mutant. Carotenoid production was only recovered when carP was transcribed upstream of carS, but not at other genomic locations, indicating a cis-acting mechanism of action on carS. However, some genes hardly affected by CarS were strongly upregulated in the carP mutant, indicating that carP may have other regulatory functions as an independent regulatory element

overall_design: To check the role of the carP lncRNA, we compared the transcriptomes of the wild strain IMI58289 and the carP deletion mutant SG268, incubated in the dark or illuminated for 60 min. Data were obtained from three independent biological replicates for each condition

last: Medina

first: Gabriel

last: Gutiérrez

first: M

last: Limón


title: Regulation effect and mechanism of Sheng-Hua-Tang on female reproductive system: from experimental transcriptomic analysis to clinical applications

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

country: Taiwan

institute: China Medical University

summary: Sheng-Hua-Tang (SHT) is commonly used to treat female illnesses, especially postpartum conditioning. However, its effects and mechanisms on female reproductive system remain unclear. The aim of the present study was to investigate the effect of SHT on female brain-ovary-uterus axis from bench to clinic.

overall_design: Mice were administrated SHT (200 mg/kg) orally for seven consecutive days. Brain, ovary, and uterus tissues were then collected for microarray analysis.


title: Specialized ribosomes in yeast as a response to oxidative stress

city: Barcelona

first: Eva Maria

last: Novoa

address: Dr. Aiguader 88

institute: Center for Genomic Regulation

summary: The yeast genome contains a substantial amount of duplicated ribosomal protein genes. Functional characterization of deletion strains of individual paralogs show that the phenotypes upon deletion are not the same for a given paralog pair, suggesting that ribosomal protein paralog genes have distinct functions and thus are not redundant. Here we aimed to explore the differential function of RPL22A and RPL22B in protein synthesis. For this aim, we compared the ribosome-bound mRNAs found in different polysomal fractions: monosome, polysomal low (2-3ribosomes/mRNA), and polysomal high (>3ribosomes/mRNA), relative to total mRNA, for 3 different yeast strains: ∆RPL22A, ∆RPL22B and wild-type. Our results show that the use of one or the other specific ribosomal paralog affects the protein synthesis rates of specific transcripts, suggesting that each ribosomal protein paralog is optimized for decoding a subset of transcripts. We also find that the ratio of these paralogs changes upon oxidative stress, and propose that ribosome heterogeneity might be employed as a strategy to tune protein translation upon oxidative stress.

overall_design: For each strain (WT, ∆RPL22A, ∆RPL22B), 4 RNA pools were sequenced (input total mRNA, monosome fraction, polysome low fraction, polysome high fraction), giving a total of 24 samples. Biological duplicates were produced. The 24 samples were sequenced in two HiSeq2500 lanes, and reads containing the same barcode from the two lanes were merged.

first: Eva

first: Helaine

middle: G

last: Vieira


title: RNA-Chromatin Interactome Reveals ncRNA Functions for Transcription Regulation in 3D Genome Organization

city: Farmington

first: Zhongyuan

last: Tian

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory for Genomic Medicine

summary: Noncoding RNAs (ncRNAs) are an emerging class of regulatory molecules with a broad range of regulatory functions believed to be mediated by ncRNA-chromatin interactions. Genome-wide understanding of ncRNA functions requires precise mapping of all ncRNAs and their target loci. Current methods for studying chromatin-associated ncRNA lack specificity or are limited to singly assessing RNAs. We devised an unbiased strategy to identify all RNA Interactions with Chromatin by Paired-End-Taging (RICh-PET) and applied this approach to characterize the Drosophila RNA-chromatin interactome. We discovered that ncRNAs primarily target promoters and enhancers in open chromatin regions in colocalization with RNAPII and other TFs, suggesting combinatorial regulatory instructions for each locus. Enzymatic nuclear digestion followed by examination of specific chromatin loci indicated that ncRNAs collectively promote chromatin accessability, RNAPII-mediated interactions and overall 3D-genome organization. Our study demonstrates that RICh-PET and related methods represent a powerful suite of tools to interrogate the genome biology of ncRNAs.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: Investigation of RNA-chromatin Interactome by RICh-PET

first: Meizhen

last: Zheng

first: Oscar-Junhong

last: Luo

first: Simon-Zhongyuan

first: Yijun

last: Ruan


title: Transcriptional and genomic occupancy profiling from MLX WT and MLX knockout mouse tissues.

city: Seattle

first: Brian

last: Freie

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: We generated mice null for MAX-like Protein X (MLX), encoded by Mlx. All male mice are sterile. We profiled testes tissue from WT versus KO mice by RNA-Seq. We performed ChIP-Seq on WT and KO testes for MLX and MAX, as well as ChIP-Seq for MLX and MAX from primary B220+ splenic B cells, and ChIP-Seq for MLX, MAX and MNT from 3T3 cell lines derived from WT and KO embryos.

overall_design: RNA-Seq and ChIP-Seq for MLX and MAX was performed on testes from MLX WT and MLX knockout (KO) mice. ChIP-Seq for MLX and MAX was performed on primary B220+ B cells from WT and KO mice. ChIP-Seq for MLX, MAX and MNT was performed on 3T3 cell ines derived from MLX WT and MLX KO embryos.

first: Patrick

last: Carroll

middle: W

first: Robert

last: Eisenman


title: The effect of nicotine on RNA sequencing of mice spermatozoa

first: Dong

last: Zhang

address: dongchuan road

institute: shanghaijiaotong university

summary: Our laboratory previous research confirmed that nicotine in cigarette smoke causes apoptosis in germ cells in the testis and it will increase the formation of autophagosomes in the cytoplasm of testicular stromal cells. In addition, nicotine, the main toxic substance in cigarette smoke, also affects telomerase activity of spermatogenic cells, shortens telomere length, and causes structural damage of chromosomes. It is worth noting that after nicotine treatment, the expression of proteins involved in cytoskeleton regulation and energy metabolism in mouse testis was significantly up-regulated, and the sperm motility of mice was improved after nicotine treatment.   To investigate the underlying mechanism, C57BL/6J mice were divided into control and nicotine treated groups. Next generation RNA sequencing and bio-informatics analysis were carried out to analysis the effects of nicotine on the RNA profile of mice spermatozoa. The results of RNA-Seq showed that the number of reads in the control group was 2089729, and the number of reads in the nicotine-treated group was 1739093, and a total of 8699 transcripts were obtained. Expression level of some pathways remarkably changed after nicotine treatment.This experimental study are helpful to understand the mechanism of the effect of nicotine on sperm and help us to provide a way to study the effection of patern nicotine exposure on offspring development.

overall_design: RNA profiles of the spermatozoa of 11-weeks old  control and nicotine treated groups mice were generated by RNA sequencing.

first: Zhongdong

last: Qiao


title: Stem cell fate choices are regulated through antagonistic control of lysosomes by MYC and TFEB [ATAC-Seq]

city: Toronto

first: Laura

last: Garcia Prat

address: 101 College street

department: Princess Margaret Cancer Centre

institute: University Health Network

summary: We show that lysosomes are antagonistically controlled by TFEB and MYC to balance catabolic and anabolic processes required for activating LT-HSC and guiding their lineage fate. TFEB-mediated induction of the endolysosomal pathway for membrane receptor degradation limits LT-HSC metabolic and mitogenic activation; this promotes quiescence and self-renewal and governs erythroid-myeloid commitment. By contrast, MYC engages biosynthetic processes while repressing lysosomal catabolism to drive LT-HSC activation. Collectively, our study identifies lysosomes as a central regulatory hub for proper and coordinated stem cell fate determination.

overall_design:
Long-term hematopoietic stem cells (LT-HSC) were sorted from human cord blood and cultured overnight before transduction with lentivirus overexpressing GP91 (CTRL) or TFEB. Six days later, BFP+ transduced cells were sorted for DNA extraction, library preparation and sequencing
Authors state that raw data will be uploaded to the EGA database.

last: Garcia-Prat


title: Nanostring miRNA expression profiling analysis for QKI-5 knockdown H1299 cells and control cells

city: Wenzhou

first: RI

last: CUI

address: University Town, Chashan

institute: Wenzhou Medical University

summary:
We used the NanoString Human nCounter miRNA expression platform to compare the miRNA expression profiles of QKI-5 knockdown H1299 cells and control cells
We found that QKI-5 knockdown significantly changed miRNA expression pattern in lung cancer cells

overall_design: Control siRNA and siRNA against QKI-5 were transfected to H1299 human lung cancer cells and total RNAs were extracted from the cells and subjected to Nanostring human ncounter miRNA assay

first: Cui

last: Ri

first: Meng

last: Wei


title: RNA-Seq for Rhesus monkey placenta

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

summary: We generated RNA-Seq data for Rhesus monkey placenta. Together with RNA-Seq and epigenomic data generated for placentas of human and mouse, we aim to understand the evolution of gene expression and regulatory elements among the placentas of different mammalian species.

overall_design: RNA-Seq data for Rhesus monkey placenta

first: Ming-an

first: Gernot

last: Wolf

first: Todd

last: Macfarlan


title: Human CD28 is essential for T-cell immunity to skin-tropic a- and g-papillomaviruses

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

summary: In humans, α-papillomavirus HPV-2 and γ-papillomavirus HPV-4 typically cause common warts. In rare patients, HPV-2 may cause striking “tree man” manifestations. We describe here a patient with the HPV-2-driven “tree man” phenotype, and two of his distant relatives with unusually severe HPV4-driven warts. Genetic, transcriptional, and histological analyses of the “tree man” lesions showed that they formed a multifocal benign epithelial tumor driven by a specific HPV-2 strain. Surprisingly, all three patients are homozygous for a mutation of an essential splice site in the CD28 gene, which encodes an activating surface receptor on T cells. They have no detectable CD28 on their T cells, which, with the exception of a small contingent of revertant memory CD4+ T cells, do not respond to CD28 stimulation. Their T cells express normal levels of other costimulatory molecules and CTLA-4, and respond to CD2 stimulation. T- and B-cell development, and responses to antigens are otherwise normal in these individuals. Finally, CD28-deficient mice are vulnerable to cutaneous infections with the μ-papillomavirus MmuPV1. This experiment of Nature shows that the control of HPV-2 and HPV-4 in human keratinocytes is dependent on the T-cell CD28 co-activation pathway, which seems to be otherwise largely redundant in host defense.

overall_design: Naive CD4+of 4 controls and 1 CD28-/- patient were negatively sorted and stimulated with various combinations of mAb-coated beads

first: Vivien

last: Béziat

first: Franck

last: Rapaport

first: Élise

last: Bandet

first: Cindy

last: Ma

first: Roya

last: Sherkat

first: Hassan

last: Rokni-Zadeh

first: Matthias

last: Titeux

first: Jiafen

last: Hu

first: Majid

last: Changi-Ashtiani

first: Ottavia

last: Delmonte

first: Andrea

last: Guenoun

first: Frédégonde

last: About

first: Geetha

last: Rao

first: Claire

last: Rouzaud

first: Jingwei

last: Li

first: Debra

last: Shearer

first: Soroosh

last: Dabiri

first: Mana

last: Momenilandi

first: Justine

last: Nammour

first: Marie-Alexandra

last: Alyanakian

first: Marianne

last: Leruez-Ville

first: David

last: Guenat

first: Mathilde

last: Bonnet des Claustres

first: Marie

last: Materna

first: Léa

last: Marcot

first: Christine

last: Soret

first: Émilie

last: Catherinot

first: Mohammed

last: Zarhate

last: Woodley

first: Mohamed

last: Jeljeli

first: Serkan

last: Belkaya

first: Lazaro

last: Lorenzo

first: Jérémie

last: Rosain

first: Fanny

last: Lanternier

first: Olivier

last: Lortholary

first: Stéphane

last: Blanche

first: Faramarz

last: Zakavi

first: Gérard

last: Orth

first: Laurent

last: Abel

first: Jean-Luc

last: Prétet

first: Nico

last: Marr

first: Sylvie

last: Fraitag

first: Luigi

last: Notarangelo

first: Alain

last: Hovnanian


title: Transcriptomic profiling of inflammatory phenotypes of severe asthma using endobronchial biopsies

city: New Lambton Heights

first: Stephany

last: Sanchez

state: NSW

address: Lot 1 Kookaburra Circuit

department: Respiratory and Sleep Medicine

country: Australia

institute: University of Newcastle

summary:
Severe asthma is a complex disease with different inflammatory phenotypes. Transcriptomic profiling has contributed to understanding the pathogenesis of asthma, especially type-2 inflammation; however, there is still poor understanding of non-eosinophilic asthma, and consequently there are limited treatment options.
The aim of this study was to determine transcriptomic profiles in endobronchial biopsies of adults with severe asthma and different inflammatory phenotypes (neutrophilic, eosinophilic and paucigranulocytic) compared with healthy controls.

overall_design: This cross-sectional study examined endobronchial biopsies from 47 adults with severe asthma and different inflammatory phenotypes; neutrophilic (n = 9), eosinophilic (n = 22) and paucigranulocytic (n = 16) and healthy controls (n=13).

last: Sánchez-Ovando

first: Jodie

middle: L

last: Simpson

first: Katherine

middle: J

last: Baines

first: Daniel

last: Barker

first: Peter

last: Wark


title: Stem cell fate choices are regulated through antagonistic control of lysosomes by MYC and TFEB

first: Laura

last: Garcia Prat

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: The Trithorax group protein ASH1 requires a combination of BAH domain and AT hooks, but not the SET domain, for mitotic chromatin binding and survival

city: Berlin

first: Leonie

last: Ringrose

address: Philippstr. 13

department: IRI Lifesciences

institute: Humboldt University Berlin

summary: The Drosophila Trithorax group (TrxG) protein ASH1 remains associated with mitotic chromatin through mechanisms that are poorly understood. ASH1 dimethylates histone H3 at lysine 36 via its SET domain. Here we identify domains of the TrxG protein ASH1 that are required for mitotic chromatin attachment in living Drosophila. Quantitative live imaging demonstrates that ASH1 requires AT hooks and the BAH domain but not the SET domain for full chromatin binding in metaphase, and that none of these domains are essential for interphase binding. Genetic experiments show that disruptions of the AT hooks and the BAH domain together, but not deletion of the SET domain alone, are lethal. Transcriptional profiling demonstrates that intact ASH1 AT hooks and the BAH domain are required to maintain expression levels of a specific set of genes, including several involved in cell identity and survival. This study identifies in vivo roles for specific ASH1 domains in mitotic binding, gene regulation and survival that are distinct from its functions as a histone methyltransferase.

overall_design: Transgenic flies expressing variants of the ASH1 protein fused to EGFP in an ash1 mutant background, were generated. RNAseq analysis was performed on 3rd instar larval wing discs of each of three variants, namely EGFP::ASH1 WT, EGFP::ASH1DBAH and EGFP::ASH1DBAH mut AT1 and compared to wing discs from wild type flies.

first: Sini

last: Juntilla


title: Multimodal single cell analysis of molecular profiles of paired tissues of cutaneous T cell lymphoma

status: Public on Jul 30 2021

first: Youzhi

last: Cheng

state: Connecticut

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

summary: Cutaneous T cell lymphoma (CTCL) is a heterogeneous group of mature T cell neoplasms characterized by the accumulation of clonal malignant CD4+ T cells in the skin. The most common variant of CTCL, Mycosis Fungoides, is confined to the skin in early stages but can be accompanied by extracutaneous dissemination of malignant T cells to the blood and lymph nodes in advanced stages of disease. Sézary Syndrome, a leukemic form of disease is characterized by significant blood involvement. Little is known about the transcriptional and genomic relationship between skin and blood residing malignant T cells in CTCL. In the present study we interrogate multiple modalities of information in single cells from matched skin and blood samples of patients with leukemic disease and healthy controls within a single workflow. By employing expanded CRISPR-compatible cellular indexing of transcriptomes and epitopes by sequencing (ECCITE-seq), we sought to compare the molecular profile of malignant clones residing in the skin and circulation of these patients across gene and protein expression modalities. We apply inferred CNV and phylogenetic analysis to examine sub-clonal heterogeneity to gain insights into the evolution and the relationship of malignant clones across tissues. Our data reveals clonal evolution at a transcriptional and genetic level within the malignant populations of individual patients. We highlight highly consistent transcriptional signatures delineating skin-derived and blood-derived malignant T cells. Analysis of these two populations suggests that environmental cues, along with genetic aberrations, contribute to transcriptional profiles of malignant T cells.

overall_design:
ECCITE-seq gene expression, antibody derived tag, and TCR clonotype profiles of matched skin and blood from 5 Sézary syndrome (SS) and leukemic Mycosis Fungoides (MF) patients and a healthy control. We also include ECCITE-seq profiles from 2 additional SS patients.

>>>Submitter states that raw data will be made available at dbGaP due to patient privacy concerns<<<

first: Sergei

last: Koralov

first: Alberto

last: Herrera

first: Anthony


title: Connection of core and and tail Mediator modules restrains transcription from TFIID-dependent promoters [ChEC-seq]

city: Bloomington

first: Gabriel

last: Zentner

state: IN

address: 915 E 3rd St

institute: Indiana University

summary: The Mediator coactivator complex is divided into four modules: head, middle, tail, and kinase. Deletion of the architectural subunit Med16 separates core Mediator (cMed), comprising the head, middle, and scaffold (Med14), from the tail. However, the direct global effects of tail/cMed disconnection are unclear. We find that rapid depletion of Med16 downregulates genes that require the SAGA complex for full expression, consistent with their reported tail dependence, but also moderately overactivates TFIID-dependent genes in a manner partly dependent on the separated tail, which remains associated with upstream activating sequences. Suppression of TBP dynamics via removal of the Mot1 ATPase partially restores normal transcriptional activity to Med16-depleted cells, suggesting that cMed/tail separation results in an imbalance in the levels PIC formation at SAGA-requiring and TFIID-dependent genes. We suggest that the preferential regulation of SAGA-requiring genes by tailed Mediator helps maintain a proper balance of transcription between these genes and those more dependent on TFIID.

overall_design: ChEC-seq of Mediator subunits in Med16 deletion or depletion strains.

first: Moustafa

last: Saleh